Dark Waters
by Star Trekker 13
Summary: When a mad scientist reawakens an old enemy: foul things emerge- as well as unexpected heroes.
1. Chapter 1

"So, in other words, the unnamed ensign got sent back to Earth against his will."

_"Wow, that must have been a hard choice."_

"Dad, you know that protocol states: 'Whenever a crew member has severe suicidal thoughts, no matter what rank they have, they must be returned to Earth for not only their own safety but also for more counseling. It is the counselor's decision, but must also have the captain's approval.' "

Just another video call with my father on a Friday. Despite the extremely long distance between the USS Excalibur and the USS Enterprise, the connection was surprisingly well.

_"Well, I just want to let you know that I'm proud of what you're doing over there."_

"Thanks, dad. And you should also be proud of what you're doing on the Enterprise. I mean, what number surgery is this? Your fiftieth? That's got to be a new record for Starfleet."

_"Jennifer McCoy, don't go bringing that up again or you're going to make me regret not recommending you for the Enterprise... And for the record, it's the fortieth."_

"I'm just saying that you need to be recognized more for your work. I mean, you did just save the Captain of your ship what, nine months ago?"

_"Another reason why I didn't recommend you for the Enterprise."_

"Dad, after what you've told me about him, I think I could handle myself against him. By the way, thank you for the Tribble you sent me, but are you sure that was a great idea?"

_"Don't worry, that one won't reproduce like crazy. Not like the ones we had. But just to be safe, don't go feeding it any grain."_

"Sure thing."

_"… Your mom would be proud of you, too."_

"Don't go bringing her up, please."

_"I'm serious, she would be."_

"I could care less for what she thinks and you know why."

_"The same reason you became a counselor-which you still refuse to tell me?"_

"Exactly."

_"Okay, forget I said anything."_

"Thanks."

Suddenly, red lights flashed in my room and sirens blared.

_"Jenny, what's going on over there?!"_

"I don't know. I'm requested on the bridge though. I have to go. I love you, daddy."

_"Love you, too, sweetheart. Be careful!"_

"Always am!"

And with that, I hung up on my father for what would be the last time in a long while, tucked my PADD under my arm, and raced for the bridge.

Now, typically, the bridge is not a place for a counselor. However, with my experience in psychoanalyzing people as well as my slight skills in diplomacy, I was usually welcome there in situations like these.

As I quickly sat in my seat (once again thanking the designers for the fact that my chair was not one with wheels), my friend in Communications, Samantha Rogers, filled me in.

"We've got an unmarked ship heading for us. It's size is far superior than ours, and it's denied all communication efforts," she said.

"Has anyone contacted Starfleet HQ yet?"

"We've sent a notice to them, but no other information yet."

"It's arriving in five seconds, Captain," said the head of Engineering.

I turned my chair to face the main screen. In an instant, an enourmous, pitch-black ship filled our sight. I was breathless from fright. It was exactly like the one my father described when Khan tried to take over and defeat Starfleet. But that was impossible. He was in cryosleep! I stealthily drew out my PADD, and took the best picture I could take. I sent it to my dad when another crew member said, "They're hailing us, sir!"

"On screen and broadcast ship-wide, for the record."

Soon, an image of a man filled the screen, covering the ship. I recognized him as Dr. Vincent Winters. He was head of the science program at Starfleet Headquarters. His silver, close cut hair slightly shone in his ship's light. Despite the fact that he was middle-aged, he was very fit.

"Dr. Winters," said the Captain to our ship, Hans Fredrickson. "That's quite a familiar ship you have there."

"Indeed it is, Captain. Starfleet repaired this ship in case there would ever be a war with the Klingons. It was not in use, so that made it very easy to steal."

"And to what do we owe the displeasure of your visit?"

"Test subjects."

"… I'm sorry?"

"I'll make this easy for your simple brain to understand. Surrender your ship, and submit yourselves to my experiments. Refuse, and I'll be forced to kill a majority of you along with taking less subjects than I hoped to gain. So, what is it going to be? Are you going to be a hero or be the fool?"

"I will not allow any of my crew to become your test subjects! We've all heard about your insane experiments, and we will not have any part of it!"

"Oh, I was afraid it would come to that. Now, let me see. Eeenie, meanie, miny, moe; let us see who's going to go!"

Suddenly, the white beams of light of a transporter shone and circled around me. I looked to Samantha, and she stared on in horror as I disappeared from sight.

Then, I found myself in a room of white. A glass window/door showed a black-clad guard in the center of the room along with other rooms similar to mine: filled with people.

I was in a prison cell.

I looked to my right, and was welcomed with sight of someone very familiar to me in only description. The same guy who had caused the Enterprise and Federation so much grief and pain. Chills went down my spine and fear clouded my heart.

The man in the cell next to me was Khan.

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><p><strong>I know that I haven't exactly finished the first Khan story that I wrote but this one was begging to be written, so my focus was spent on this. Don't worry, I will go back to the first one and complete it.<strong>

**Oh, and I want to say thanks to DrAgOnLOvEr34 for being a wonderful editor/revisor/best friend! Go check out her fanfictions because they are really amazing!**

**Keep Khan and Kling-On!**

**-Star Trekker 13**


	2. Chapter 2

Khan, the mass murderer himself, didn't say a word-not a single one. And that was the scariest thing about him. He just stared at me, sizing me up. Every part of my body was trembling with fright but I held his gaze. I had to try my best to not appear afraid, but it felt like I was failing. Finally, he turned away and the glass wall between us fogged up and became white.

"He doesn't do anything."

I jumped as I realized that I wasn't alone. There, in the corner, wearing a black tunic (which the shirt was far too big for her small size) was an 18-year-old girl. Her short, pixie-cut hair, which I assumed would have been a normal bright auburn, was dull from dirt and grime. She wore a black necklace around her neck. Her skin was a tiny bit oily. Her green eyes were also dull. I wondered if that was going to happen to me.

"He just stares at the newcomers-hardly says a word. No one knows why."

I made my way over to the girl and kneeled in front of her.

"What's your name?"

"A-113. Group 7-"

"No, your real name. Tell me your real name and which ship you came from."

"… Amelia Gillan. USS Bradbury."

"Jennifer McCoy. USS Excalibur. You can call me Jenny."

"That's a pretty name, but you better hang on to it."

"Why?" I asked, taking her pulse.

"Your name doesn't matter here. Same goes for your rank and which ship you come from. Everything gets taken. You're just given a letter, number, and group. All that matters is how strong you are."

"Amy, can I call you Amy?"

She nodded her head and I my train of thought resumed, "You're pretty young to be working on a Starfleet ship."

"I managed to get into the advanced program."

"I can tell; how old are you?"

"Seventeen."

"Well, I was pretty close. I thought you were eighteen."

"That's what everyone says."

"Now, Amy, I want you to tell me. Why does Dr. Winters want test subjects? What is he doing with us?"

"I don't know. He doesn't say what these tests are for. He doesn't say anything about it. He just inserts these weird solutions into us. So far, for me at least, it's been penicillin. But other people have been getting different things."

"And Dr. Winters hasn't said one word about this?"

"Well, I did hear him say one thing about it. He said something about making the ultimate super-human."

"How many people are here?"

"I don't know. Thirty tops? The ones on the ship are not the only ones."

"What?! You mean there are more?" I asked in a loud whisper.

"Well, I see the guards take some out of their cells and Dr. Winters telling them to place them in escape pods and jettison them to different planets. I don't remember the names."

"Please try to remember!"

Before Amelia could reply, the door to our cell opened. When I turned my head, to see a man who could be the devil himself at this very moment, along with two fellow demons.

"Well, Miss McCoy, I'm so glad you could join us."

"Considering the fact that I had no choice, I can't say the same."

The insane doctor lowly chuckled and said, "Very much like your captain, you are. Trying to be brave but instead acting very stupid. Look where that got him and his crew."

"What did you do to them?"

"Look outside your window. I do believe that's a part of your bridge floating past."

Sure enough, I turned around, and was stunned by the site. The area around this prison ship was littered with the wreckage of the USS Excalibur.

I turned back and raised my fist to punch the crap out of this man. Instead, one of his goons, grabbed it, punched me in the face, and sent me to the ground.

"Hmm, a bit of fire in you. That will be useful."

I gripped my jaw, double-checking that it was still in place.

"These are your new clothes. You have five minutes."

I heard a bunch of fabric being thrown to the ground before the door shut again. I felt Amy's hand on my shoulder.

"I know you're hurt, but you need to put those on."

"I'm okay. No teeth missing, I'm good. Can you block the view while I change?"

Amy nodded, and I proceeded to get the new uniform on. After I put on the tunic and pants, I looked at the necklace.

"C-1989?"

"That means you're in group C, and your number is 1989. I don't think it actually means that there were 1,988 people before you."

"Well, that's reassuring," I said, putting it on. "Do we really have to wear them?"

"That's not really a question. I saw one guy who took it off and ended up getting tased by the guards."

"Well, that's very reassuring. Now what?" I asked, retying my hair into a ponytail.

"Your hair is going to go. Every girl gets their hair cut if it's longer than a pixie cut."

"Ha. Like hell that's going to happen," I said, sitting down criss cross on the floor.

"You won't have a choice. If you resist them, they knock you out and give you a horrible hair cut."

"And that's the worst thing that happens here?"

"Just, please, trust me and just go with it."

"Fine, for you, I will. That doesn't mean I'm going to like it."

Then, at exactly five minutes, not a second over nor under, the mad scientist with his goons were back.

"Glad to see that you are ready to begin, Miss McCoy."

I wasn't going to gratify that with a response. As the guards grabbed my upper arms and drug me out, my feet struggling to find balance to catch up, I couldn't erase this feeling of dread inside of me.

What was I being brought into?

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><p><strong>I'm glad to see that there are some people interested in this. Again, special thanks to DrAgOnLOvEr 34 for taking time off of her busy schedule to look over new chapters and story ideas. :)<strong>

**Now for a bit of self promoting. Don't forget to check out my profile page for updates on my latest stories. I'll try to update everything else before I add anything else to this story. Also, I have a poll up on my page and I would really appreciate it if you guys could take a few minutes to vote on it. It could change the outcome of one of my new stories.**

**Thanks for reading!**

**-Star Trekker 13**


	3. Update: Happy Holidays!

**Hello everyone! Happy Holidays to all! Whether you celebrate Christmas, Hanukkah, or even Kwanzaa, may you be merry this time of year.**

**Now, some of you may have been wondering where the latest chapters to my stories have been. Well, this update will be posted on all of my stories so all of you can see it.**

**Now, I have been busy with college, sorority life (I'm a member of Alpha Xi Delta), final exams, and preparing for the Christmas season. Tonight, I have a sort of gift/announcement for all of you.**

**With the exception of "Whose Side is Right?", I will provide an update to every story by January 1st, 2015.**

**As for "Whose Side is Right?", I know a lot of you have been waiting for the latest chapter to this. Some of you may know that I have started a new Khan story called "Dark Waters". I have decided, after a lot of thought, that "Whose Side is Right?" will serve as a prequel to this story, and will have an update once "Dark Waters" is finished. You have my word on that.**

**Now, as for me, I will be spending Christmas Eve writing a Castiel x Reader for my Deviantart (same name as here), eating chicken lips with my family, and waiting for Santa's arrival. Yes, I am officially hooked on Supernatural and Castiel. XD**

**Again, Happy Holidays and I can't wait to hear more reviews from all of you. :)**

**-Star Trekker 13**


	4. Chapter 3

"I kept staring at my reflection, running my hand through my now pixie cut short hair. It was pretty oily considering how many days I had gone without a shower. Granted, the day they gave me that uniform, they threw some of that prison dry soap all over me, and according to Amelia, they let us shower once every week, but it didn't matter. I still felt really gross.

"Speaking of Amelia, they took her a while ago and she still hasn't returned. I do hope the worst hasn't happened.

It turned out my first day was just to get shot up with antibiotics and to have a tracker anklet put on. Despite having a bit of training as a nurse, and having a dad who is a doctor, I was never a big fan of needles. They ended up getting five men to hold me down in order to receive the medicine.

Despite being here for five days, I still had no idea what was happening here. And speaking of my dad, I hoped he got the picture of the Vengeance that I sent him. I couldn't imagine what was rolling through his head. There was a reason why I preferred him to my mother. To be honest, I hated my mother's guts for everything she did. Now, my dad probably thought I was dead.

I just hoped that I would get out of here to see him again.

"For some reason, I didn't take you as a shallow person," Khan said, making the wall that separated us transparent, so instead of seeing my reflection, I saw his face.

I really hated it when he did that. He's been doing it the past few days, just popping up like that. This is the first time he actually said something to me.

"Well, excuse me for not being used to short hair," I replied, realizing that I still kept tugging at it, as if one solid pull would make it all grow out again.

"And here I thought you were a woman of scholar."

"And here I thought you were a narcissistic jerk who didn't care about those who are—oh, how did you put it—beneath you."

"I can see your relation to the Enterprise now. You're just like them: stupid, pretending to have the morale high ground, not thinking of the greater consequences, and incredibly foolish."

"My father is the head doctor on the _U.S.S. Enterprise_. Be thankful that there's a wall between us now. When I get the chance, you will regret saying those things when I smack you a new one," I bitterly replied.

Khan smirked, as if he was pleased to receive an emotional response out of me.

"That matters not. Chances are that you will not survive the tests ahead."

"I'll think you'll find that I have a strong will to live."

"That will change once you see the state of your friend."

"…. What happened to her?"

I heard an electric hum behind me, and saw a transparent wall separate the cell.

"You will see soon enough," he said, and the wall between us became solid white again.

I focused my attention on Amelia, who was just tossed in by three guards. She was curled in a fetal position and her hands clutched her head.

"Amelia? Are you okay?" I asked, inching closer to the new wall.

She kept wriggling on the ground, letting out small cries of pain.

"Amelia! Please answer me!" I shouted, pounding my hands on the glass between us.

She didn't respond, and kept wriggling until finally, with a shrill scream, her hair turned into flames!

There was only one thought running through my head as I threw myself away from the sight before me: 'What the hell?!'

I watched as she tried to stand and more fire came out of her hands. As soon as she did, mini spray nozzles came out of her walls and started spraying a mist in the room. Soon enough, Amelia fainted from the after effects.

Now, I had a basic idea of what this mad man Winters had in store for all of us. But if Amelia had the ability to use fire….. What was in store for me?

Short, I know, but I had a deadline to meet.

*UPDATE* Sorry about all the lines of coding. I guess thats what comes from uploading a chapter on your iPad instead of the computer. Well, I learned my lesson.

Hope everyone had a great New Year's!


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